More time available in bonuses today than the spread of the top 10 in the 20km individual start.
If FIS were in charge of cycling, Peter Sagan, Michael Matthews and Edvald Boasson Hagen would be battling out the Grand Tours.
That's not the right comparison you make.
Top 10 in the mass start were separated by 1 minute. Top 10 in the sprint by less than 30 seconds.
Also, how would you change to bonus system in sprints?
You can't give time bonuses only for the first 3 as you punish the others making them do an extra effort for nothing. And you should somehow reward everyone who passed the qualification as they still do an extra effort
Also, you're other comparison is way out of line. None of the 3 you mentioned is even top 50 on the hard mountain stages. In comparison to the likes Diggins and Klaebo, they are comfortably top 10 and actual favourites for some distance races.
Valverde, if you ask me, is decent comparison to both and he podiumed all the GTs and won one.
If we compare distance races to hard GC stages and sprints to TTs, in cycling you don't see the likes of Mas or Cancellara dominate GC's, you're looking for all-rounders (or rarely extremely gifted climbers) the same goes to TdS. You don't get the likes of Pellegrino or Holund dominate, you get all-rounders (Diggins, Klaebo, Boergen, Bolshunov, Cologna...) and rarely extremely gifted distance skiers (like Bauer and Johaug) win.
I mean, all the bad things aside, Peter Northug was really all-around skier and he won only one TdS.
When I think about it, the biggest problem aren't the big sprint bonuses, but the presence of 2 mass starts and one pursuit instead of one more 15-20 km individual race.